Blender 2.71 parenting objects transforms objects
Typically the scaling does not change when entering the game engine. This is different, when you are playing an animation or change something via Python.

My advice to you is to void scaling (especially the in-homogeneousscaling) at the parents. 

If you need scaled meshes, you can create the object tree by using empties as parent. You can parent the previous parent objects to the empties. This way they are no parents anymore and you can scale them without side effects. Just make sure the empties are not scaled.

Example:

Frame (scaled)
- Button A (scaled)
- Button B (scaled)


changed to:

Root (Unscaled Empty)
- Frame (scaled)
- Button A (scaled)
- Button B (scaled)


or

Root (Unscaled Empty)
- Frame (scaled)
- Button Base (Unscaled Empty)
  - Button A (scaled)
  - Button B (scaled)